Skipjack (SJT) ( Katsuwonus pelamis ) is a medium-sized, pelagic, highly dispersive tuna species that occurs widely across tropical and subtropical waters. SJT constitute the largest tuna fishery in the Indian Ocean and are currently managed as a single stock. Patterns of genetic variation in a mtDNA gene and six microsatellite loci were examined to test for stock structure in the northwestern Indian Ocean. 324 individuals were sampled from five major fishing grounds around Sri Lanka and from single sites in the Maldive Islands and the Laccadive Islands. Phylogenetic reconstruction of mtDNA revealed two coexisting divergent clades in the region. Analysis of molecular variance (AMOVA) of mtDNA data revealed significant genetic differentiation among sites (ΦST = 0.2029, P < 0.0001), also supported by spatial AMOVA results. AMOVA of microsatellite data also showed significant differentiation among most sampled sites (FST = 0.0256, P < 0.001), consistent with the mtDNA pattern. STRUCTURE analysis of the microsatellite data revealed two differentiated stocks. While both marker types examined identified two genetic groups, microsatellite analysis indicates that the sampled SJT are likely to represent individuals sourced from discrete breeding grounds that are mixed in feeding grounds in Sri Lankan waters.

Yellowfin tuna are currently considered by the member nations of the Indian Ocean Tuna Commission to constitute a single stock in the Indian Ocean due to a lack of knowledge about yellowfin tuna population structure in this region. Previous studies of Indian Ocean yellowfin tuna based on morphology and fisheries data have hinted at the presence of multiple stocks in the region, and further, that stocks may mix in the north western Indian Ocean around Sri Lanka. To better understand the genetic stock structure of yellowfin tuna in the north western Indian Ocean, we examined genetic variation in 285 yellowfin individuals collected over a period of 4 years from six fishing grounds around Sri Lanka and a single fishing ground in the Maldive Islands. We screened variation in both the mitochondrial ATPase 6 and 8 region (498 bp) and three microsatellite loci. Significant genetic differentiation was detected among sites for mitochondrial DNA (Φ ST = 0.1285, P < 0.001) and at two microsatellite loci (F ST = 0.0164, P < 0.001 and F ST = 0.0064, P < 0.001), while spatial analysis of molecular variance of mtDNA data identified three genetically heterogenous groups namely; western, south eastern and all remaining sites. These results suggest the possibility that genetically discrete yellowfin tuna populations may be present in the north western Indian Ocean.

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor ∼1 × 10 6 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

The native Asian oyster, Crassostrea ariakensis is one of the most common and important Crassostrea species that occur naturally along the coast of East Asia. Molecular species diagnosis is a prerequisite for population genetic analysis of wild oyster populations because oyster species cannot be discriminated reliably using external morphological characters alone due to character ambiguity. To date there have been few phylogeographic studies of natural edible oyster populations in East Asia, in particular this is true of the common species in Korea C. ariakensis. We therefore assessed the levels and patterns of molecular genetic variation in East Asian wild populations of C. ariakensis from Korea, Japan, and China using DNA sequence analysis of five concatenated mtDNA regions namely; 16S rRNA, cytochrome oxidase I, cytochrome oxidase II, cytochrome oxidase III, and cytochrome b. Two divergent C. ariakensis clades were identified between southern China and remaining sites from the northern region. In addition, hierarchical AMOVA and pairwise U ST analyses showed that genetic diversity was discontinuous among wild populations of C. ariakensis in East Asia. Biogeographical and historical sea level changes are discussed as potential factors that may have influenced the genetic heterogeneity of wild C. ariakensis stocks across this region.

Stock enhancement involves the augmentation of wild populations with hatchery-reared recruits. Stock enhancement generally also includes a postrelease monitoring program which tracks stocked individuals within the fishery, and this relies on having a means to identify the likely origin of recaptured fish (e.g., physical, otolith, or genetic tags). This study reports the application of sibship analysis to retrospectively infer the origin of Mulloway (Argyrosomus japonicus) within stocked estuaries, when other means of identification were not available. Eight cohorts of Mulloway were stocked into two estuaries, across a seven-year period, but only some of the fish released during the program were physically marked with chemical otolith stains. Fish were sampled from stocked estuaries (mostly through an angler-based sampling program) and genotyped for six microsatellite loci, alongside 129 fish sampled from nonstocked estuaries. The presence of multiple sibs within the mixed populations in stocked estuaries was used to infer the origin of captured fish, against a background of sibship for known-origin individuals (verified by otolith marks) and sibship levels within unstocked estuaries. The analysis suggested hatchery-reared fish could have contributed 9% of individuals sampled from the augmented populations (7% when corrected for background sibship). The proportion of fish inferred to be of hatchery origin decreased with size (likely due to mortality and migration), and the expected contribution rates for hatchery-reared fish differed among cohorts. The results highlight that sibship analysis may be useful for retrospective genetic evaluation of stocked estuaries.

Skipjack tuna (SJT), Katsuwonus pelamis is the largest tuna fishery in all the major oceans around the world, and the largest marine fishery in Sri Lanka. Knowledge of genetic population structure and effective population size of SJT in the Indian Ocean and other major oceans, however, is still lacking for improved management practices and conservation strategies. We developed microsatellite genetic markers using SJT found around Sri Lanka in the Indian Ocean, and characterized one tri-and seven tetra-nucleotide microsatellite loci isolated from enriched genomic libraries from SJT, to provide tools for addressing both conservation and fisheries management strategies. Analysis of these eight microsatellite markers in two populations of SJT from eastern Sri Lanka (n = 44) and the Maldives Islands (n = 53) showed that all eight microsatellites were polymorphic with an average number of alleles per locus of 11.80 (range 5-27). Expected heterozygosities at marker loci ranged from 0.450 to 0.961. No significant linkage disequilibrium was detected among any loci pairs. These markers are currently being used to characterize population structure and extent of natural gene flow in SJT populations from the eastern and western Indian Ocean.

Giant freshwater prawn (GFP; Macrobrachium rosenbergii) aquaculture has expanded rapidly since 1990. Most local culture industries, however, have developed in an unsystematic way. Fiji has a small culture industry producing the ‘Anuenue’ strain; however, performance of this strain has never been systematically evaluated. Recently, some Fijian farmers have reported declines in stock productivity. The current project evaluated the relative performance of three exotic strains with different genetic backgrounds from Malaysia, Indonesia and Vietnam, against the ‘local’ strain in Fiji in a 4 × 3 replicated pond trial experiment. A total of 5827 prawns were harvested after 143 days growout. Individual growth rate and relative survival of the Fiji strain were not statistically different from any of the introduced strains, but Vietnam strain was superior to that of the Malaysia strain. Genetic diversity showed significant differences in variability among strains, with the Malaysian strain displaying the lowest genetic diversity. Indonesia strain showed that females were reaching maturation earlier than other strains and were smaller in size. This study suggests that Malaysian and Indonesian strains would constitute a poor choice for Fiji, whereas the Vietnam strain consistently performed well on all criteria measured. High variation among replicate ponds within strains unfortunately confounded among‐strain variation.